The founder and president of Kynikos Associates said in a "Squawk Box" interview that he's shorting Dunkin' Brands DNKN and Burger King's parent Restaurant Brands International QSR-CA .

"We've been short these things for about a year," Chanos said.

On the news, shares of Dunkin' saw an initial 5 percent spike lower in premarket trading before recovering those losses. Dunkin' had been up before Chanos' comments.

Shares of Restaurant Brands — owner of Burger King, Tim Hortons, and Popeyes Louisiana Kitchen — sank about 3 percent on the news and then pared some of those declines.

In making his case, Chanos said price-to-earnings ratios for restaurant stocks have been going "higher, higher, and higher as restaurants themselves have struggled."

"At some point, that's has to come to an end," he predicted.

"This is part of a broader theme ... the franchisers versus the franchisees," Chanos said. He said he doesn't like what he calls "this asset light idea" of these companies not owning their restaurants while "basically clipping the coupons, collecting royalties" from the franchises.

"We're also short a number of these asset light models," he said, but did not reveal any names beyond Restaurant Brands and Dunkin'.

On Thursday morning, Dunkin' Brands reported adjusted quarterly earnings of 62 cents per share — 9 cents better than expectations. However, revenue of $301.3 million fell short of estimates.

Shares of Dunkin' — owner of Dunkin' Donuts and Baskin-Robbins — were 3.5 percent lower in 2018, but were about 13.3 percent higher in the past 12 months as of Wednesday's close.

Shares of Restaurant Brands were 10.7 percent lower for 2018 and were down about 6 percent in the past 12 months as of Wednesday's close.

Neither Restaurant Brands nor Dunkin' Brands were immediately available to respond to CNBC's requests for comment on Chanos' interview.

Kynikos Associates, with more than $2 billion in assets under management, saw its short-only fund down 12 percent last year, according to sources familiar with the matter. Kynikos' hedge fund was up 22 percent last year, sources said, adding both funds are about flat in 2018.